0s autopkgtest [19:03:59]: starting date and time: 2025-03-15 19:03:59+0000 0s autopkgtest [19:03:59]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:03:59]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ziqmhkfb/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade segemehl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-23.secgroup --name adt-plucky-s390x-segemehl-20250315-190359-juju-7f2275-prod-proposed-migration-environment-20-19fdee70-fe5c-4239-a711-4fbc14245f85 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 81s autopkgtest [19:05:20]: testbed dpkg architecture: s390x 81s autopkgtest [19:05:20]: testbed apt version: 2.9.33 81s autopkgtest [19:05:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 81s autopkgtest [19:05:20]: testbed release detected to be: None 82s autopkgtest [19:05:21]: updating testbed package index (apt update) 82s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 83s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 83s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 83s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 83s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 83s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 83s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 83s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 83s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 83s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 83s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 83s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 83s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 83s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 83s Fetched 1073 kB in 1s (1130 kB/s) 84s Reading package lists... 84s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s Calculating upgrade... 85s Calculating upgrade... 85s The following packages were automatically installed and are no longer required: 85s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 85s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 85s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 85s linux-tools-6.11.0-8-generic 85s Use 'sudo apt autoremove' to remove them. 85s The following packages will be upgraded: 85s pinentry-curses python3-jinja2 strace 85s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Need to get 652 kB of archives. 85s After this operation, 27.6 kB of additional disk space will be used. 85s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 86s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 86s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 86s Fetched 652 kB in 1s (1041 kB/s) 86s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81428 files and directories currently installed.) 86s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 86s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 86s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 86s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 86s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 86s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 86s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 86s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 86s Setting up strace (6.13+ds-1ubuntu1) ... 86s Processing triggers for man-db (2.13.0-1) ... 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Solving dependencies... 87s The following packages will be REMOVED: 87s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 87s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 87s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 87s linux-tools-6.11.0-8-generic* 87s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 87s After this operation, 167 MB disk space will be freed. 88s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81428 files and directories currently installed.) 88s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 88s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 88s Removing libpython3.12t64:s390x (3.12.9-1) ... 88s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 88s Removing libnsl2:s390x (1.3.0-3build3) ... 88s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 88s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 88s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 89s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 89s Processing triggers for libc-bin (2.41-1ubuntu1) ... 89s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56328 files and directories currently installed.) 89s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 89s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 89s autopkgtest [19:05:28]: upgrading testbed (apt dist-upgrade and autopurge) 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 90s Starting 2 pkgProblemResolver with broken count: 0 90s Done 90s Entering ResolveByKeep 90s 90s Calculating upgrade... 90s The following packages will be upgraded: 90s libc-bin libc-dev-bin libc6 libc6-dev locales 90s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Need to get 9512 kB of archives. 90s After this operation, 8192 B of additional disk space will be used. 90s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 91s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 91s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 91s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 91s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 91s Preconfiguring packages ... 91s Fetched 9512 kB in 1s (8782 kB/s) 91s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 91s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 92s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 92s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 92s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 92s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 92s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 92s Setting up libc6:s390x (2.41-1ubuntu2) ... 92s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 92s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 92s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 92s Setting up libc-bin (2.41-1ubuntu2) ... 92s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 92s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 92s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 92s Setting up locales (2.41-1ubuntu2) ... 92s Generating locales (this might take a while)... 93s en_US.UTF-8... done 93s Generation complete. 93s Setting up libc-dev-bin (2.41-1ubuntu2) ... 93s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 93s Processing triggers for man-db (2.13.0-1) ... 94s Processing triggers for systemd (257.3-1ubuntu3) ... 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s Starting pkgProblemResolver with broken count: 0 95s Starting 2 pkgProblemResolver with broken count: 0 95s Done 96s Solving dependencies... 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 96s autopkgtest [19:05:35]: rebooting testbed after setup commands that affected boot 114s autopkgtest [19:05:53]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 117s autopkgtest [19:05:56]: @@@@@@@@@@@@@@@@@@@@ apt-source segemehl 118s Get:1 http://ftpmaster.internal/ubuntu plucky/universe segemehl 0.3.4-5build2 (dsc) [2106 B] 118s Get:2 http://ftpmaster.internal/ubuntu plucky/universe segemehl 0.3.4-5build2 (tar) [244 kB] 118s Get:3 http://ftpmaster.internal/ubuntu plucky/universe segemehl 0.3.4-5build2 (diff) [7960 B] 119s gpgv: Signature made Mon Apr 1 08:00:00 2024 UTC 119s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 119s gpgv: Can't check signature: No public key 119s dpkg-source: warning: cannot verify inline signature for ./segemehl_0.3.4-5build2.dsc: no acceptable signature found 119s autopkgtest [19:05:58]: testing package segemehl version 0.3.4-5build2 119s autopkgtest [19:05:58]: build not needed 120s autopkgtest [19:05:59]: test run-unit-test: preparing testbed 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s Starting pkgProblemResolver with broken count: 0 120s Starting 2 pkgProblemResolver with broken count: 0 120s Done 120s The following NEW packages will be installed: 120s libdeflate0 libhts3t64 libhtscodecs2 segemehl 121s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 121s Need to get 875 kB of archives. 121s After this operation, 2046 kB of additional disk space will be used. 121s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 121s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libhtscodecs2 s390x 1.6.1-2 [91.0 kB] 121s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x libhts3t64 s390x 1.21+ds-1 [479 kB] 121s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x segemehl s390x 0.3.4-5build2 [259 kB] 121s Fetched 875 kB in 1s (1334 kB/s) 121s Selecting previously unselected package libdeflate0:s390x. 122s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 122s Preparing to unpack .../libdeflate0_1.23-1_s390x.deb ... 122s Unpacking libdeflate0:s390x (1.23-1) ... 122s Selecting previously unselected package libhtscodecs2:s390x. 122s Preparing to unpack .../libhtscodecs2_1.6.1-2_s390x.deb ... 122s Unpacking libhtscodecs2:s390x (1.6.1-2) ... 122s Selecting previously unselected package libhts3t64:s390x. 122s Preparing to unpack .../libhts3t64_1.21+ds-1_s390x.deb ... 122s Unpacking libhts3t64:s390x (1.21+ds-1) ... 122s Selecting previously unselected package segemehl. 122s Preparing to unpack .../segemehl_0.3.4-5build2_s390x.deb ... 122s Unpacking segemehl (0.3.4-5build2) ... 122s Setting up libhtscodecs2:s390x (1.6.1-2) ... 122s Setting up libdeflate0:s390x (1.23-1) ... 122s Setting up libhts3t64:s390x (1.21+ds-1) ... 122s Setting up segemehl (0.3.4-5build2) ... 122s Processing triggers for libc-bin (2.41-1ubuntu2) ... 122s Processing triggers for man-db (2.13.0-1) ... 123s autopkgtest [19:06:02]: test run-unit-test: [----------------------- 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading database sequences. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: 1 database sequences found. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: total length of db sequences: 250 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: assigning all reads to default read group 'A1'. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: additional read group default values ' SM:sample1 LB:library1 PU:unit1 PL:illumina' 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reads assigned to read group 'A1' 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: compiled sam header. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alphabet of size (5): ACGT 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: size of db sequence: 251 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: constructing suftab. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusort: classify. 123s init bit array of 32 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusort: getting bit. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: bit alurusort: alloc B of size 124. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusort: initbitarray of size 124. 123s init bit array of 16 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusort: Qmaxdist in cl of size 251. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: enter alurusort: substringsort. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: setting bit array to zero 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: allocating space for buckets and buffers 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: memsetting 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: substring sort ... ok 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: checking valbitarray. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: enter Tprime calculation. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: tprime: init arrays. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: tprime: scan B 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: tprime: iterating i=251 elements with lenB=124. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: tprime: exit 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: enter alursortint. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: classify int. 123s init bit array of 16 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: getting bit. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: init bcktsA. 123s init bit array of 16 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: countingsort. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: countingsortint: init buffers and A 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: setting buffer to zero 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: countsortint: scanning buffer (1 of 3) 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: countsortint: scanning buffer (2 of 3) 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: countsortint: scanning buffer (3 of 3) 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: countsortint: scanning buffer (to set borders) 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: countsortint: exiting 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: Sorting type S suffixes. Init bcktsB. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: 55 69 124. 123s 123s init bit array of 7 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: arrayB: allocating B with 55 elements. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: arrayB: iterating to lenA=124. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: arrayB: exiting 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: enter Qmaxdist. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: enter Qdist. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: enter distCount. 123s init bit array of 16 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: enter get listsS. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: getlistsS: memsetting list of 121 elements. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: getlistsS: iter up to 124. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: getlistsS: scan A 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: getlistsS: set accidst 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: getlistsS: exiting 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: freeing stuff. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: enter sortlistsS. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: sortlistS: allocating stuff. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: sortlistS: iterating 55 elems. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: sortlistS: looping 121 elems. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: sortlistS: iterating 124 elems. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: sortlistsS: exiting happily! 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: enter tprime. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: tprime: init arrays. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: tprime: scan B 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: tprime: iterating i=124 elements with lenB=55. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: tprime: exit 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: enter alurusortint. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: classify int. 123s init bit array of 7 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: getting bit. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: init bcktsA. 123s init bit array of 7 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: countingsort. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: countingsortint: init buffers and A 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: setting buffer to zero 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: countsortint: scanning buffer (1 of 3) 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: countsortint: scanning buffer (2 of 3) 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: countsortint: scanning buffer (3 of 3) 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: countsortint: scanning buffer (to set borders) 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: countsortint: exiting 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: Sorting type S suffixes. Init bcktsB. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: 27 28 55. 123s 123s init bit array of 4 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: arrayB: allocating B with 27 elements. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: arrayB: iterating to lenA=55. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: arrayB: exiting 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: enter Qmaxdist. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: enter Qdist. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: enter distCount. 123s init bit array of 7 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: enter get listsS. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: getlistsS: memsetting list of 54 elements. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: getlistsS: iter up to 55. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: getlistsS: scan A 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: getlistsS: set accidst 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: getlistsS: exiting 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: freeing stuff. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: enter sortlistsS. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: sortlistS: allocating stuff. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: sortlistS: iterating 27 elems. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: sortlistS: looping 54 elems. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: sortlistS: iterating 55 elems. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: sortlistsS: exiting happily! 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: alurusortint: valbitarraysortedS. 123s init bit array of 7 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reconstructintS. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reconstruct: init. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reconstruct: iteration over 124 elems. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reconstruct: scan B (size: 55). 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reconstruct: exit. 123s init bit array of 16 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: enter reconstruction. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reconstruct: init. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reconstruct: iteration over 251 elems. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reconstruct: scan B (size: 124). 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reconstruct: exit. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: enter aluruSuffixArrayL start. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: aluruSuffixArrayL: initalizning arrays. 123s init bit array of 32 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: aluruSuffixArrayL: memsetting count. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: aluruSuffixArrayL: setting b. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: aluruSuffixArrayL: iteration. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: aluruSuffixArrayL: exit ok. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: constructing inv_suftab (251). 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: inv_suftab constructed. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: constructing lcp. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: deleting inv_suftab 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: constructing child tab. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: constructing suffix links. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: constructing id. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: constructing suflinks - bottom up. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: constructing suflinks - top down. 123s suflink construction. pushes: 177, maxstack: 7 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: building the suffix array has taken 0.000000 seconds. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: total length of suffix array was 250. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: writing suffix array 'index.idx' to disk. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: Mapping stats: 123s total mapped (%) unique (%) multi (%) split (%) 123s all 0 0 nan% 0 nan% 0 nan% 0 nan% 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: 123s Goodbye. 123s "Wir sind hier nicht in Seattle Dirk!" (Tocotronic) 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading queries in 'myseq.fa'. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: 1 query sequences found. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading database sequences. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: 1 database sequences found. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: total length of db sequences: 250 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: assigning all reads to default read group 'A1'. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: additional read group default values ' SM:sample1 LB:library1 PU:unit1 PL:illumina' 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reads assigned to read group 'A1' 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: compiled sam header. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading suffix array 'index.idx' from disk. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading lcpc/vtab. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading childtab. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading suflinks. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading lsint id. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: read suffix array 'index.idx' with 251 elements. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: md5 keys of index and db match. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading the suffix array has taken 0.000000 seconds. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: matching w/ suffixarray has taken 0.000000 seconds. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: Mapping stats: 123s total mapped (%) unique (%) multi (%) split (%) 123s all 1 0 0.00% 0 0.00% 0 0.00% 0 0.00% 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: 123s Goodbye. 123s "Wir sind hier nicht in Seattle Dirk!" (Tocotronic) 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading queries in 'seq2.fa'. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: 1 query sequences found. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading database sequences. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: 1 database sequences found. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: total length of db sequences: 250 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: assigning all reads to default read group 'A1'. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: additional read group default values ' SM:sample1 LB:library1 PU:unit1 PL:illumina' 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reads assigned to read group 'A1' 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: compiled sam header. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading suffix array 'index.idx' from disk. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading lcpc/vtab. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading childtab. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading suflinks. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading lsint id. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: read suffix array 'index.idx' with 251 elements. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: md5 keys of index and db match. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: reading the suffix array has taken 0.000000 seconds. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: writing multi splits to 'seq2.mult.bed' 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: writing sngle splits to 'seq2.sngl.bed' 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: writing trans splits to 'seq2.trns.txt' 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: matching w/ suffixarray has taken 0.000000 seconds. 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: Mapping stats: 123s total mapped (%) unique (%) multi (%) split (%) 123s all 1 0 0.00% 0 0.00% 0 0.00% 0 0.00% 123s [SEGEMEHL] Sat Mar 15 19:07:28 2025: 123s Goodbye. 123s "Wir sind hier nicht in Seattle Dirk!" (Tocotronic) 123s PASS Test 124s autopkgtest [19:06:03]: test run-unit-test: -----------------------] 124s run-unit-test PASS 124s autopkgtest [19:06:03]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 124s autopkgtest [19:06:03]: @@@@@@@@@@@@@@@@@@@@ summary 124s run-unit-test PASS 129s nova [W] Using flock in prodstack6-s390x 129s Creating nova instance adt-plucky-s390x-segemehl-20250315-190359-juju-7f2275-prod-proposed-migration-environment-20-19fdee70-fe5c-4239-a711-4fbc14245f85 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 129s nova [W] Timed out waiting for b073be6e-f837-4c8a-9660-49a790a984d9 to get deleted.